Question

Researchers have described the “binary patterning” of polar and nonpolar amino acids in the sequences of proteins. In their code, polar and charged residues like D, N, E, Q, K, H, and R are represented as open circles (○) and nonpolar residues like F, L, I, M, and V as closed circles (●). Thus, a polypeptide with the sequence asp-ile-his-phe-gln would be represented as ○●○●○. Researchers analyzed the binary patterns of isolated secondary structure elements (short pieces) from native proteins. A sequence with the pattern ○●●○○●●○○●●○ forms an amphipathic alpha helix that has a nonpolar face and a polar face. A sequence with the pattern ○●○●○● forms an amphipathic beta strand. Explain these observations by discussing the structures of helices and sheets.

Answer 1

To answer these questions one should observe the periodicity and repeating patterns in the sequence.

1. ○●●○○●●○○●●○ has a nonpolar residue after every 3 or 4 positions, which is similar to the alpha-helical repeat of 3.6 residues per turn. Hence, peptides with this sequence pattern forms amphiphilic alpha-helices. This structure self-assembles into bundles like shape and the nonpolar faces of the individual helices are buried in the core of these bundles.

2. The next sequence with the alternating pattern ○●○●○● have a periodicity of 2. This is similar to the structural repeats of beta-strands with successive side chains pointing up-down-up-down, etc. Such sequences form amphiphilic beta-strands that bury their nonpolar faces by aggregating into large beta-sheet structures. Hence, all the polar residues will point at one direction and all the non polar at the other direction.

The image below will give a better understanding of the binary patterning and structures.

The first one is alpha helix and the other one is beta strand.